Configuring STARS on Bio-Linux
Setting up the environment and databases
Installing the stars_setup.pl script
Install the stars_setup.pl script to /usr/local/bin from pubmlst.org. This can be done by typing the following (this is one line of code and there are no spaces in the URL):
sudo wget -nc -nd -P/usr/local/bin http://pubmlst.org/software/scripts/ stars_setup/download/stars_setup.pl
Now make the script executable to all users:
sudo chmod a+x /usr/local/bin/stars_setup.pl
The system is now set up. Further details of the stars_setup.pl script can be found here.
Setting up your STARS environment
From a normal user account type:
stars_setup.pl -s
This creates the STARS/staden directories in your home directory.
Setting up a database
You can setup a database for species supported on pubmlst.org. The script automatically downloads a template database to create your new database. The templates are set up to automatically clip MLST alleles and look up allele numbers from the MLST websites. Type:
stars_setup.pl -c NM-KEITH-01 (use your own naming scheme here)
You will be presented with a menu of supported species. Select the one you want and the system will be configured for you. This configuration includes modifying your .zshrc start up script to set the default database - open a new shell for the modifications to take affect (or type 'source .zshrc' from your home directory).